org.hkijena.jipipe.plugins.ilastik.nodes

Class IlastikAutoContextAlgorithm

java.lang.Object

org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

org.hkijena.jipipe.api.nodes.JIPipeGraphNode

org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeSingleIterationAlgorithm

org.hkijena.jipipe.plugins.ilastik.nodes.IlastikAutoContextAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable, IlastikEnvironmentAccessNode

public class IlastikAutoContextAlgorithm
extends JIPipeSingleIterationAlgorithm
implements IlastikEnvironmentAccessNode

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IlastikAutoContextAlgorithm.OutputParameters

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.BaseDirectoryChangedEventEmitter, JIPipeGraphNode.BaseDirectoryChangedEventListener, JIPipeGraphNode.NodeSlotsChangedEvent, JIPipeGraphNode.NodeSlotsChangedEventEmitter, JIPipeGraphNode.NodeSlotsChangedEventListener, JIPipeGraphNode.Serializer

Nested classes/interfaces inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterChangedEventEmitter, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEventEmitter, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEvent, JIPipeParameterCollection.ParameterUIChangedEventEmitter, JIPipeParameterCollection.ParameterUIChangedEventListener

Field Summary

Fields

Modifier and Type	Field and Description
static JIPipeDataSlotInfo	OUTPUT_SLOT_FEATURES_STAGE_1
static JIPipeDataSlotInfo	OUTPUT_SLOT_FEATURES_STAGE_2
static JIPipeDataSlotInfo	OUTPUT_SLOT_INPUT_STAGE_1
static JIPipeDataSlotInfo	OUTPUT_SLOT_INPUT_STAGE_2
static JIPipeDataSlotInfo	OUTPUT_SLOT_LABELS_STAGE_1
static JIPipeDataSlotInfo	OUTPUT_SLOT_LABELS_STAGE_2
static JIPipeDataSlotInfo	OUTPUT_SLOT_PROBABILITIES_ALL_STAGES
static JIPipeDataSlotInfo	OUTPUT_SLOT_PROBABILITIES_STAGE_1
static JIPipeDataSlotInfo	OUTPUT_SLOT_PROBABILITIES_STAGE_2
static JIPipeDataSlotInfo	OUTPUT_SLOT_SIMPLE_SEGMENTATION_STAGE_1
static JIPipeDataSlotInfo	OUTPUT_SLOT_SIMPLE_SEGMENTATION_STAGE_2
static JIPipeDataSlotInfo	OUTPUT_SLOT_UNCERTAINTY_STAGE_1
static JIPipeDataSlotInfo	OUTPUT_SLOT_UNCERTAINTY_STAGE_2
static String	PROJECT_TYPE

Fields inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
IlastikAutoContextAlgorithm(IlastikAutoContextAlgorithm other)
IlastikAutoContextAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
void	getEnvironmentDependencies(List<JIPipeEnvironment> target) Gathers all known external environments
IlastikAutoContextAlgorithm.OutputParameters	getOutputParameters()
OptionalIlastikEnvironment	getOverrideEnvironment()
IlastikProjectValidationMode	getProjectValidationMode()
boolean	isCleanUpAfterwards()
void	onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event) Triggered when a parameter is changed within the slot configuration.
void	reportValidity(JIPipeValidationReportContext reportContext, JIPipeValidationReport report) Generates a validity report
protected void	runIteration(JIPipeMultiIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setCleanUpAfterwards(boolean cleanUpAfterwards)
void	setOverrideEnvironment(OptionalIlastikEnvironment overrideEnvironment)
void	setProjectValidationMode(IlastikProjectValidationMode projectValidationMode)

Methods inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeSingleIterationAlgorithm

generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getIgnoredAnnotationColumns, getParallelizationBatchSize, isAllowEmptyIterationStep, isParameterUIVisible, isParameterUIVisible, runParameterSet, runPassThrough, supportsParallelization

Methods inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

createUIInputSlotIconDescriptionMenuItems, getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, run

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, onDeserialized, runPassThrough, setEnabled, setPassThrough, setRuntimePartition, setSkipped

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

archiveTo, canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, emitNodeSlotsChangedEvent, fromJson, getAliasIdInParentGraph, getBaseDirectory, getBaseDirectoryChangedEventEmitter, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getCustomName, getDependencies, getDisplayName, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getName, getNewScratch, getNodeSlotsChangedEventEmitter, getNodeUILocationPerViewModePerCompartment, getNodeUILocationWithin, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProject, getProjectCompartment, getProjectDataDirs, getProjectDirectory, getRuntimeProject, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getTextDescription, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, onSlotConfigurationChanged, renderInputSlots, renderOutputSlots, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setNodeUILocationPerViewModePerCompartment, setNodeUILocationWithin, setNodeUILocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots

Methods inherited from class org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, onParameterStructureChanged, onParameterUIChanged, registerSubParameter, registerSubParameters

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.hkijena.jipipe.plugins.ilastik.environments.IlastikEnvironmentAccessNode

getConfiguredIlastikEnvironment, reportConfiguredIlastikEnvironmentValidity

Methods inherited from interface org.hkijena.jipipe.api.nodes.iterationstep.JIPipeIterationStepAlgorithm

generateDataBatchesDryRun

Methods inherited from interface org.hkijena.jipipe.api.nodes.JIPipeAdaptiveParametersAlgorithm

installUIOverrideParameterEditor, installUIParameterOptions

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

deserializeFromJsonNode, emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, serializeToJsonFile, serializeToJsonGenerator, serializeToJsonString, setParameter

Methods inherited from interface org.hkijena.jipipe.api.validation.JIPipeValidatable

generateValidityReport

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterUIChangedEventListener

onParameterUIChanged

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterStructureChangedEventListener

onParameterStructureChanged

Field Detail

PROJECT_TYPE

public static final String PROJECT_TYPE

See Also:

Constant Field Values

OUTPUT_SLOT_PROBABILITIES_STAGE_1

public static final JIPipeDataSlotInfo OUTPUT_SLOT_PROBABILITIES_STAGE_1

OUTPUT_SLOT_PROBABILITIES_STAGE_2

public static final JIPipeDataSlotInfo OUTPUT_SLOT_PROBABILITIES_STAGE_2

OUTPUT_SLOT_PROBABILITIES_ALL_STAGES

public static final JIPipeDataSlotInfo OUTPUT_SLOT_PROBABILITIES_ALL_STAGES

OUTPUT_SLOT_SIMPLE_SEGMENTATION_STAGE_1

public static final JIPipeDataSlotInfo OUTPUT_SLOT_SIMPLE_SEGMENTATION_STAGE_1

OUTPUT_SLOT_SIMPLE_SEGMENTATION_STAGE_2

public static final JIPipeDataSlotInfo OUTPUT_SLOT_SIMPLE_SEGMENTATION_STAGE_2

OUTPUT_SLOT_UNCERTAINTY_STAGE_1

public static final JIPipeDataSlotInfo OUTPUT_SLOT_UNCERTAINTY_STAGE_1

OUTPUT_SLOT_UNCERTAINTY_STAGE_2

public static final JIPipeDataSlotInfo OUTPUT_SLOT_UNCERTAINTY_STAGE_2

OUTPUT_SLOT_FEATURES_STAGE_1

public static final JIPipeDataSlotInfo OUTPUT_SLOT_FEATURES_STAGE_1

OUTPUT_SLOT_FEATURES_STAGE_2

public static final JIPipeDataSlotInfo OUTPUT_SLOT_FEATURES_STAGE_2

OUTPUT_SLOT_LABELS_STAGE_1

public static final JIPipeDataSlotInfo OUTPUT_SLOT_LABELS_STAGE_1

OUTPUT_SLOT_LABELS_STAGE_2

public static final JIPipeDataSlotInfo OUTPUT_SLOT_LABELS_STAGE_2

OUTPUT_SLOT_INPUT_STAGE_1

public static final JIPipeDataSlotInfo OUTPUT_SLOT_INPUT_STAGE_1

OUTPUT_SLOT_INPUT_STAGE_2

public static final JIPipeDataSlotInfo OUTPUT_SLOT_INPUT_STAGE_2

Constructor Detail

IlastikAutoContextAlgorithm

public IlastikAutoContextAlgorithm(JIPipeNodeInfo info)

IlastikAutoContextAlgorithm

public IlastikAutoContextAlgorithm(IlastikAutoContextAlgorithm other)

Method Detail

runIteration

protected void runIteration(JIPipeMultiIterationStep iterationStep,
                            JIPipeIterationContext iterationContext,
                            JIPipeGraphNodeRunContext runContext,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeSingleIterationAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeSingleIterationAlgorithm

Parameters:

iterationStep - The data interface

iterationContext - The iteration context

runContext - the run context

progressInfo - the progress from the run

reportValidity

public void reportValidity(JIPipeValidationReportContext reportContext,
                           JIPipeValidationReport report)

Description copied from interface: JIPipeValidatable

Generates a validity report

Specified by:

reportValidity in interface JIPipeValidatable

Overrides:

reportValidity in class JIPipeAlgorithm

Parameters:

reportContext - the report context

report - the report to be added to

getProjectValidationMode

public IlastikProjectValidationMode getProjectValidationMode()

setProjectValidationMode

public void setProjectValidationMode(IlastikProjectValidationMode projectValidationMode)

getOutputParameters

public IlastikAutoContextAlgorithm.OutputParameters getOutputParameters()

isCleanUpAfterwards

public boolean isCleanUpAfterwards()

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

getOverrideEnvironment

public OptionalIlastikEnvironment getOverrideEnvironment()

Specified by:

getOverrideEnvironment in interface IlastikEnvironmentAccessNode

setOverrideEnvironment

public void setOverrideEnvironment(OptionalIlastikEnvironment overrideEnvironment)

onParameterChanged

public void onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event)

Description copied from class: JIPipeGraphNode

Triggered when a parameter is changed within the slot configuration. Triggers a JIPipeGraphNode.NodeSlotsChangedEvent

Specified by:

onParameterChanged in interface JIPipeParameterCollection.ParameterChangedEventListener

Overrides:

onParameterChanged in class JIPipeParameterSlotAlgorithm

Parameters:

event - generated event

getEnvironmentDependencies

public void getEnvironmentDependencies(List<JIPipeEnvironment> target)

Description copied from class: JIPipeGraphNode

Gathers all known external environments

Overrides:

getEnvironmentDependencies in class JIPipeGraphNode

Parameters:

target - the list where the external environments will be gathered